Add Read, Glob, and Grep tool permissions to D4D Assistant (#72)

The D4D Assistant needs these fundamental tools to operate:
- Read: Read files from the repository and /tmp/ai-input/user-prompt.txt
- Glob: Find files by pattern when exploring the codebase
- Grep: Search file contents for metadata extraction

Without Read permission, the assistant cannot even read the user's
prompt from /tmp/ai-input/user-prompt.txt, causing permission errors
in GitHub Actions.

This fixes the permission error:
'Claude requested permissions to read from /tmp/ai-input/user-prompt.txt,
but you haven't granted it'

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude <[email protected]>

Author: justaddcoffee

.github/workflows/d4d-agent.yml

@@ -197,4 +197,4 @@ jobs:
           enable-obo-scripts: 'true'
           enable-python-tools: 'true'
           python-packages: 'aurelian jinja2-cli "wrapt>=1.17.2"'
-          claude-allowed-tools: '["FileEdit", "Edit", "Edit(*)", "Write", "Bash", "Bash(git:*)", "Bash(gh:*)", "Bash(poetry:*)", "Bash(make:*)", "Bash(python:*)", "Bash(uv:*)", "Bash(echo:*)", "Bash(cat:*)", "Bash(mkdir:*)", "Bash(grep:*)", "Bash(head:*)", "Bash(tail:*)", "Bash(sort:*)", "Bash(curl:*)", "mcp__github__*", "mcp__artl__*", "WebSearch", "WebFetch"]'
+          claude-allowed-tools: '["Read", "Glob", "Grep", "FileEdit", "Edit", "Edit(*)", "Write", "Bash", "Bash(git:*)", "Bash(gh:*)", "Bash(poetry:*)", "Bash(make:*)", "Bash(python:*)", "Bash(uv:*)", "Bash(echo:*)", "Bash(cat:*)", "Bash(mkdir:*)", "Bash(grep:*)", "Bash(head:*)", "Bash(tail:*)", "Bash(sort:*)", "Bash(curl:*)", "mcp__github__*", "mcp__artl__*", "WebSearch", "WebFetch"]'